Rationale: In this day of exploding bioinformatics information
from genomics and proteomics, it is ever more important to be conversant
with macromolecular three-dimensional structure, and how it relates to
protein and nucleic acid function and rational drug design. This workshop will
enable participants to find published molecular structure data, and visualize
and interpret 3D molecular structure. Participants will be enabled to
incorporate computer visualization of protein, DNA, and RNA into their
teaching and research.

Software: The central tool for this workshop is Protein Explorer
(www.proteinexplorer.org). Protein Explorer is free,
operates on Windows or Macintosh (also
linux), and is much easier to use, yet much
more powerful than RasMol. Protein Explorer has been adopted for visualization
of macromolecular 3D structure by the Protein Data Bank
(www.pdb.org).

Level & Pace: This workshop is designed for
educators and biological scientists familiar with basic biochemistry, but with no
previous molecular visualization software experience.
It progresses rapidly to powerful tools that will be of interest
to researchers, including specialists in protein structure and bioinformatics.
Experienced participants are encouraged to work at their own speed,
ahead of the group -- there is plenty of power in Protein Explorer to discover!

Hyperlinks: To click the hyperlinks below, go to this document on the web,

http://www.umass.edu/molvis/workshop/ubarc01.htm

Tuesday April 24.
Basics.
How to use Protein Explorer to visualize structural features of
proteins and nucleic acids.
Observations may be recorded on a form provided.

FirstView

Use of the mouse to rotate the molecule; clicking to identify atoms.

Identifying and becoming familiar with the computer representations for chains, backbones, disulfide bonds, solvent, and ligands.

Aligning two or more chains or molecules, and how to view the alignment.

The CE site
cl.sdsc.edu/ce.html
will align any two protein chains quickly and easily
(but hetero atoms are discarded).

Swiss PDB Viewer
www.expasy.ch/spdbv/mainpage.html
can align anything
(one or more than one chains), selecting any subset of atoms for
the alignment (other atoms following), and retaining hetero
atoms. The results can be saved as a PDB file. It will need
manual editing to separate models with MODEL [N] and ENDMDL
records so that Protein Explorer can distinguish the models.